BioC 3.5: CHECK report for HIBAG on malbec2

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings HIBAG_1.12.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/HIBAG.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HIBAG/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HIBAG’ version ‘1.12.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘HIBAG’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

* installing *source* package ‘HIBAG’ ...
** libs
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c HIBAG.cpp -o HIBAG.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c LibHLA.cpp -o LibHLA.o
g++ -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o HIBAG.so HIBAG.o LibHLA.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/HIBAG.Rcheck/HIBAG/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (HIBAG)

name	user	system	elapsed
HIBAG-package	1.004	0.016	1.026
hlaAllele	0.012	0.000	0.014
hlaAlleleDigit	0.016	0.000	0.016
hlaAlleleSubset	0.016	0.000	0.018
hlaAssocTest	0.920	0.008	0.927
hlaAttrBagging	0.464	0.000	0.464
hlaBED2Geno	0.152	0.008	0.161
hlaCheckAllele	0.000	0.000	0.001
hlaCheckSNPs	0.056	0.000	0.057
hlaCombineAllele	0.02	0.00	0.02
hlaCombineModelObj	0.412	0.000	0.412
hlaCompareAllele	0.636	0.004	0.646
hlaConvSequence	3.196	0.048	3.254
hlaErrMsg	0.004	0.000	0.000
hlaFlankingSNP	0.004	0.000	0.005
hlaGDS2Geno	0.080	0.004	0.102
hlaGeno2PED	0.068	0.008	0.079
hlaGenoAFreq	0.000	0.000	0.004
hlaGenoCombine	0.052	0.000	0.053
hlaGenoLD	0.856	0.004	0.860
hlaGenoMFreq	0.004	0.000	0.006
hlaGenoMRate	0.008	0.000	0.010
hlaGenoMRate_Samp	0.004	0.000	0.005
hlaGenoSubset	0.008	0.000	0.009
hlaGenoSwitchStrand	0.088	0.000	0.088
hlaLociInfo	0.004	0.000	0.005
hlaMakeSNPGeno	0.024	0.000	0.027
hlaModelFiles	0.164	0.004	0.165
hlaModelFromObj	0.080	0.004	0.083
hlaOutOfBag	0.512	0.000	0.514
hlaParallelAttrBagging	0.144	0.008	1.419
hlaPredMerge	0.520	0.000	0.519
hlaPublish	0.756	0.004	0.760
hlaReport	0.732	0.000	0.731
hlaSNPID	0.008	0.000	0.007
hlaSampleAllele	0.008	0.000	0.008
hlaSplitAllele	0.044	0.000	0.043
hlaSubModelObj	0.088	0.000	0.092
hlaUniqueAllele	0.008	0.000	0.008
plot.hlaAttrBagObj	0.216	0.004	0.221
predict.hlaAttrBagClass	0.704	0.004	0.711
print.hlaAttrBagClass	0.188	0.000	0.188
summary.hlaSNPGenoClass	0.008	0.000	0.009

BioC 3.5: CHECK report for HIBAG on malbec2

Summary

Command output